After some searching, I found that it was a known bug which would be too costly to fix (see http://bugs.php.net/bug.php?id=20993). There was supposed to be some documentation on this behaviour on this page:

"Due to peculiarities of the internal workings of PHP, if a reference is made to a single element of an array and then the array is copied, whether by assignment or when passed by value in a function call, the reference is copied as part of the array. This means that changes to any such elements in either array will be duplicated in the other array (and in the other references), even if the arrays have different scopes (e.g. one is an argument inside a function and the other is global)! Elements that did not have references at the time of the copy, as well as references assigned to those other elements after the copy of the array, will behave normally (i.e. independent of the other array)."

However, this paragraph appears to have been removed from this page at some point, presumably because it was a bit obscure. The comments section seem to be a proper place for this, though.